Here is where I am - I have thrown switches, moved the train a little, thrown more switches, and now I am totally lost. I can't get around upstairs anymore. A nudge would be appreciated.

You are at the entrance to the underground train station at Atrona, at sector E-3. To the west, the platform leads to a stairway down to the lower level. To the east, you see a doorway along the north wall, and a walkway leads over the train tracks to the southeast. The map shows another walkway across the tracks to the southwest, but it appears to have collapsed. The stairway to the north turns to the west and heads back up to the exterior building.

The train is partway through the west gate, and the east portion of it occupies sectors A-6 and B-6.